move perl modules to lib/perl5

Arabidopsis-Information-Portal · Jun 27, 2012 · 71b1fe3 · 71b1fe3
1 parent ad10a4d
commit 71b1fe3
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Showing 40 changed files with 9 additions and 9 deletions.
diff --git a/bin/bam-to-json.pl b/bin/bam-to-json.pl
@@ -64,7 +64,7 @@ =head1 OPTIONS
 use warnings;
 
 use FindBin qw($Bin);
-use lib "$Bin/../lib";
+use lib "$Bin/../lib/perl5";
 use JBlibs;
 
 use Pod::Usage;

diff --git a/bin/biodb-to-json.pl b/bin/biodb-to-json.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 use strict;
 use FindBin qw($RealBin);
-use lib "$RealBin/../lib";
+use lib "$RealBin/../lib/perl5";
 use JBlibs;
 
 use Bio::JBrowse::Cmd::BioDBToJson;

diff --git a/bin/draw-basepair-track.pl b/bin/draw-basepair-track.pl
@@ -70,7 +70,7 @@ =head1 OPTIONS
 use warnings;
 
 use FindBin qw($Bin);
-use lib "$Bin/../lib";
+use lib "$Bin/../lib/perl5";
 use JBlibs;
 
 use File::Basename;

diff --git a/bin/flatfile-to-json.pl b/bin/flatfile-to-json.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 use strict;
 use FindBin qw($RealBin);
-use lib "$RealBin/../lib";
+use lib "$RealBin/../lib/perl5";
 use JBlibs;
 
 use Bio::JBrowse::Cmd::FlatFileToJson;

diff --git a/bin/generate-names.pl b/bin/generate-names.pl
@@ -40,7 +40,7 @@ =head1 OPTIONS
 use warnings;
 
 use FindBin qw($Bin);
-use lib "$Bin/../lib";
+use lib "$Bin/../lib/perl5";
 use JBlibs;
 
 use Fcntl ":flock";

diff --git a/bin/prepare-refseqs.pl b/bin/prepare-refseqs.pl
@@ -66,7 +66,7 @@ =head1 OPTIONS
 use POSIX;
 use Getopt::Long;
 
-use lib "$Bin/../lib";
+use lib "$Bin/../lib/perl5";
 use JBlibs;
 
 use JsonGenerator;

diff --git a/bin/remove-track.pl b/bin/remove-track.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 
 use FindBin '$RealBin';
-use lib "$RealBin/../lib";
+use lib "$RealBin/../lib/perl5";
 use JBlibs;
 
 use Bio::JBrowse::Cmd::RemoveTrack;

diff --git a/bin/ucsc-to-json.pl b/bin/ucsc-to-json.pl
@@ -93,7 +93,7 @@ =head1 EXAMPLE
 use warnings;
 
 use FindBin qw($Bin);
-use lib "$Bin/../lib";
+use lib "$Bin/../lib/perl5";
 use JBlibs;
 
 use Pod::Usage;

diff --git a/bin/wig-to-json.pl b/bin/wig-to-json.pl
@@ -86,7 +86,7 @@ =head1 OPTIONS
 use warnings;
 
 use FindBin qw($Bin);
-use lib "$Bin/../lib";
+use lib "$Bin/../lib/perl5";
 use JBlibs;
 
 use File::Basename;

diff --git a/lib/ArrayRepr.pm → lib/perl5/ArrayRepr.pm b/lib/ArrayRepr.pm → lib/perl5/ArrayRepr.pm
diff --git a/lib/Bio/FeatureIO/bed.pm → lib/perl5/Bio/FeatureIO/bed.pm b/lib/Bio/FeatureIO/bed.pm → lib/perl5/Bio/FeatureIO/bed.pm
diff --git a/lib/Bio/JBrowse/Cmd.pm → lib/perl5/Bio/JBrowse/Cmd.pm b/lib/Bio/JBrowse/Cmd.pm → lib/perl5/Bio/JBrowse/Cmd.pm
diff --git a/lib/Bio/JBrowse/Cmd/BioDBToJson.pm → lib/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm b/lib/Bio/JBrowse/Cmd/BioDBToJson.pm → lib/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm
diff --git a/lib/Bio/JBrowse/Cmd/FlatFileToJson.pm → lib/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm b/lib/Bio/JBrowse/Cmd/FlatFileToJson.pm → lib/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm
diff --git a/lib/Bio/JBrowse/Cmd/NCFormatter.pm → lib/perl5/Bio/JBrowse/Cmd/NCFormatter.pm b/lib/Bio/JBrowse/Cmd/NCFormatter.pm → lib/perl5/Bio/JBrowse/Cmd/NCFormatter.pm
diff --git a/lib/Bio/JBrowse/Cmd/RemoveTrack.pm → lib/perl5/Bio/JBrowse/Cmd/RemoveTrack.pm b/lib/Bio/JBrowse/Cmd/RemoveTrack.pm → lib/perl5/Bio/JBrowse/Cmd/RemoveTrack.pm
diff --git a/lib/Bio/JBrowse/FeatureStream.pm → lib/perl5/Bio/JBrowse/FeatureStream.pm b/lib/Bio/JBrowse/FeatureStream.pm → lib/perl5/Bio/JBrowse/FeatureStream.pm
diff --git a/lib/Bio/JBrowse/FeatureStream/BioPerl.pm → ...erl5/Bio/JBrowse/FeatureStream/BioPerl.pm b/lib/Bio/JBrowse/FeatureStream/BioPerl.pm → ...erl5/Bio/JBrowse/FeatureStream/BioPerl.pm
diff --git a/...io/JBrowse/FeatureStream/GFF3_LowLevel.pm → ...io/JBrowse/FeatureStream/GFF3_LowLevel.pm b/...io/JBrowse/FeatureStream/GFF3_LowLevel.pm → ...io/JBrowse/FeatureStream/GFF3_LowLevel.pm
diff --git a/lib/ExternalSorter.pm → lib/perl5/ExternalSorter.pm b/lib/ExternalSorter.pm → lib/perl5/ExternalSorter.pm
diff --git a/lib/FastaDatabase.pm → lib/perl5/FastaDatabase.pm b/lib/FastaDatabase.pm → lib/perl5/FastaDatabase.pm
diff --git a/lib/FeatureTrack.pm → lib/perl5/FeatureTrack.pm b/lib/FeatureTrack.pm → lib/perl5/FeatureTrack.pm
diff --git a/lib/GenomeDB.pm → lib/perl5/GenomeDB.pm b/lib/GenomeDB.pm → lib/perl5/GenomeDB.pm
diff --git a/lib/ImageTrack.pm → lib/perl5/ImageTrack.pm b/lib/ImageTrack.pm → lib/perl5/ImageTrack.pm
diff --git a/lib/ImageTrackRenderer.pm → lib/perl5/ImageTrackRenderer.pm b/lib/ImageTrackRenderer.pm → lib/perl5/ImageTrackRenderer.pm
diff --git a/lib/IntervalStore.pm → lib/perl5/IntervalStore.pm b/lib/IntervalStore.pm → lib/perl5/IntervalStore.pm
diff --git a/lib/JBlibs.pm → lib/perl5/JBlibs.pm b/lib/JBlibs.pm → lib/perl5/JBlibs.pm
diff --git a/lib/JsonFileStorage.pm → lib/perl5/JsonFileStorage.pm b/lib/JsonFileStorage.pm → lib/perl5/JsonFileStorage.pm
diff --git a/lib/JsonGenerator.pm → lib/perl5/JsonGenerator.pm b/lib/JsonGenerator.pm → lib/perl5/JsonGenerator.pm
diff --git a/lib/LazyNCList.pm → lib/perl5/LazyNCList.pm b/lib/LazyNCList.pm → lib/perl5/LazyNCList.pm
diff --git a/lib/LazyPatricia.pm → lib/perl5/LazyPatricia.pm b/lib/LazyPatricia.pm → lib/perl5/LazyPatricia.pm
diff --git a/lib/NCLSorter.pm → lib/perl5/NCLSorter.pm b/lib/NCLSorter.pm → lib/perl5/NCLSorter.pm
diff --git a/lib/NCList.pm → lib/perl5/NCList.pm b/lib/NCList.pm → lib/perl5/NCList.pm
diff --git a/lib/NameHandler.pm → lib/perl5/NameHandler.pm b/lib/NameHandler.pm → lib/perl5/NameHandler.pm
diff --git a/lib/TiledImage.pm → lib/perl5/TiledImage.pm b/lib/TiledImage.pm → lib/perl5/TiledImage.pm
diff --git a/lib/TiledImage/DBPrimStorage.pm → lib/perl5/TiledImage/DBPrimStorage.pm b/lib/TiledImage/DBPrimStorage.pm → lib/perl5/TiledImage/DBPrimStorage.pm
diff --git a/lib/TiledImage/MemoryPrimStorage.pm → lib/perl5/TiledImage/MemoryPrimStorage.pm b/lib/TiledImage/MemoryPrimStorage.pm → lib/perl5/TiledImage/MemoryPrimStorage.pm
diff --git a/lib/TiledImage/demo-tiledimage.pl → lib/perl5/TiledImage/demo-tiledimage.pl b/lib/TiledImage/demo-tiledimage.pl → lib/perl5/TiledImage/demo-tiledimage.pl
diff --git a/lib/TiledImage/gdtile.sql → lib/perl5/TiledImage/gdtile.sql b/lib/TiledImage/gdtile.sql → lib/perl5/TiledImage/gdtile.sql
diff --git a/lib/TrackImage.pm → lib/perl5/TrackImage.pm b/lib/TrackImage.pm → lib/perl5/TrackImage.pm